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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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OpenRefine Resource Report Resource Website 50+ mentions |
OpenRefine (RRID:SCR_021305) | data processing software, software resource, software application | Open source software Java tool for working with data. Used for loading data, cleaning up data, transforming data from one format into another and extending it with web services and external data. | Wikidata, data wrangling, loading data, cleaning up data, transforming data | is related to: Wikidata | DOI:10.3163/1536-5050.101.3.020 | Free, Available for download, Freely available | Wikidata_Q5583871 | https://www.wikidata.org/wiki/Q5583871, https://github.com/OpenRefine/OpenRefine | SCR_021305 | openrefine, Google Refine | 2026-08-12 10:52:18 | 50 | ||||||
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Hierarchical Data Modeling Framework Resource Report Resource Website 1+ mentions |
Hierarchical Data Modeling Framework (RRID:SCR_021303) | HDMF | data processing software, software application, software toolkit, software resource | Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data. | Hierarchical data, data models, reading data, writing data, unified data format, different storage backends, Python object, data, data standards |
is used by: PyNWB is related to: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Documentation Utilities is related to: HDMF Common Schema |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely available | SCR_021303 | 2026-08-12 10:52:33 | 1 | ||||||||
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FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | data processing software, software resource, software application | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; NIAID R21 AI115014; Welch Foundation ; NSF Graduate Research Fellowship DGE 0940902; NDSEG Fellowship |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-08-12 10:52:02 | 6 | |||||
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OpenComet Resource Report Resource Website 50+ mentions |
OpenComet (RRID:SCR_021826) | data processing software, image analysis software, software resource, software application | Software tool to quantify comet parameters while studying DNA strand breaks. Automated tool for comet assay image analysis. | quantify comet parameters, DNA strand breaks, comet assay image analysis | PMID:24624335 | Free, Available for download, Freely available | SCR_021826 | 2026-08-12 10:52:24 | 55 | ||||||||||
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BarensLab Mini-Atlas Resource Report Resource Website 1+ mentions |
BarensLab Mini-Atlas (RRID:SCR_021115) | data or information resource, reference atlas, atlas, mni atlas | Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature. | Phenotypic variation, transcriptomic cell types, mouse motor cortex, morpho-electric phenotypes, mouse primary motor cortex, analysis code, preprocessed data, exonic gene counts, intronic gene counts, extracted electrophysiological features, extracted morphological features, z-profiles, raw data, cellular taxonomy, neuron, morphological reconstruction | is related to: BICCN | DOI:10.1101/2020.10.19.343129v1 | Free, Freely available | SCR_021115 | 2026-08-12 10:52:29 | 6 | |||||||||
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viral_seq Resource Report Resource Website 1+ mentions |
viral_seq (RRID:SCR_018515) | data processing software, software resource, software application | Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis. | Processing viral data, next generation sequencing data, viral data, sequencing, HIV drug resistance analysis, Primer ID sequencing, data | Free, Available for download, Freely available | https://github.com/ViralSeq/viral_seq | SCR_018515 | 2026-08-12 10:52:09 | 2 | ||||||||||
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ARTS biomarker Resource Report Resource Website 10+ mentions |
ARTS biomarker (RRID:SCR_019288) | data processing software, software resource, software application | Software tool as automated biomarker that outputs score linked to likelihood person sufferring from arteriolosclerosis based on brain MRI data and basic demographic information. MRI data processing pipeline and classifier are packaged into software container.Users do not need to perform any image processing, and are only required to install Singularity to run ARTS. | Automated biomarker, score output, arteriolosclerosis, brain MRI data, demographic information, | Restricted | SCR_019288 | ARTS | 2026-08-12 10:52:25 | 29 | ||||||||||
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EphysExtraction Resource Report Resource Website 1+ mentions |
EphysExtraction (RRID:SCR_018193) | data processing software, software resource, software application | Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features. | electrophysiological parameter, extract parameter, neuron parameter, voltage trace, data | Free, Available for download, Freely available | SCR_018193 | 2026-08-12 10:52:02 | 3 | |||||||||||
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HTStream Resource Report Resource Website 10+ mentions |
HTStream (RRID:SCR_018354) | data processing software, software resource, software application | Software tool as quality control and processing pipeline for High Throughput Sequencing data. Uses tab delimited fastq format that allows for streaming from application to application. Interoperable with other standard Linux tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Next Generation Sequencing, data processing, quality control, data preprocessing | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018354 | 2026-08-12 10:52:07 | 13 | |||||||||||
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plusTipTracker Resource Report Resource Website 10+ mentions |
plusTipTracker (RRID:SCR_021890) | data processing software, image analysis software, software resource, software application | Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences. | microtubule tracking, microtubule dynamics, microtubule dynamics measurement, plusTIP marker, live cell image sequences | NIGMS U01 GM67230 | PMID:21821130 | Free, Available for download, Freely available | SCR_021890 | 2026-08-12 10:52:38 | 10 | |||||||||
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DecodingDynamic Resource Report Resource Website 1+ mentions |
DecodingDynamic (RRID:SCR_021099) | data or information resource, software resource, source code | Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex. | ECoG, neural networks, semantics, replicating analyses, data, code, notebooks, human ventral anterior temporal cortex, semantic code | Medical Research Council Programme ; European Research Council |
DOI:10.1101/695049 | Free, Freely available | SCR_021099 | 2026-08-12 10:52:29 | 1 | |||||||||
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TERL Resource Report Resource Website 1+ mentions |
TERL (RRID:SCR_022064) | data processing software, software resource, software application | Software tool for classification of transposable elements by convolutional neural networks. Preprocesses and transforms one dimensional sequences into two dimensional space data, image like data of sequences, and apply it to deep convolutional neural networks. | classification of transposable elements, convolutional neural networks, one dimensional sequences, two dimensional space data, | DOI:10.1093/bib/bbaa185 | Free, Available for download, Freely available | SCR_022064 | Transposable Elements Pepresentation Learner | 2026-08-12 10:52:50 | 3 | |||||||||
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halSynteny Resource Report Resource Website 1+ mentions |
halSynteny (RRID:SCR_018127) | data processing software, software resource, software application | Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment. | Conserved synteny, block construction method, genome alignment, DAG based reconstruction, synteny block, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:halSynteny | https://bio.tools/halSynteny | SCR_018127 | Hierarchical Alignment Format Synteny | 2026-08-12 10:52:03 | 4 | |||||||
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Smart-seq2 Multi-Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) | data processing software, software toolkit, software resource, software application | The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. | Single cell data, Smart seq2 technology, scRNAseq data, Smart-seq2 assay data, data processing | is related to: Human Cell Atlas | Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_multisample | SCR_018920 | 2026-08-12 10:52:10 | 4 | |||||||||
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BALBES Resource Report Resource Website 1+ mentions |
BALBES (RRID:SCR_018763) | standalone software, software application, software toolkit, software resource | Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement. | Molecular replacement pipeline, protein structure, solving protein structure, x-ray crystallographic data, molecular replacement, molecular replacement in CCP4, solving crystal structure, automated system, no user intervention, model searching, refinement |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: CCP4 |
Wellcome Trust ; NIGMS R01 GM069758 |
PMID:18094476 | Free, Available for download, Freely available | SCR_018763 | 2026-08-12 10:52:09 | 1 | ||||||||
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | data processing software, software resource, software application | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891, https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html | SCR_018527 | 2026-08-12 10:52:09 | 8 | |||||||||
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DeepFly3D Resource Report Resource Website 1+ mentions |
DeepFly3D (RRID:SCR_021402) | data processing software, image analysis software, software resource, software application | Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose. | Image annotation, pose tracking, pose estimation, motor circuit, behavioral measure, accurate 3D pose estimation, OpenBehavior |
is listed by: OpenBehavior is related to: DeepFly3D project |
DOI:10.7554/elife.48571 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepfly3d/ | SCR_021402 | 2026-08-12 10:52:35 | 1 | ||||||||
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imzMLConverter Resource Report Resource Website 1+ mentions |
imzMLConverter (RRID:SCR_021642) | data processing software, software resource, software application | Software tool for generating imzML. Allows conversion to imzML mass spectrometry imaging standard utilising mzML mass spectrometry standard as intermediary format. | Mass spectrometry imaging data, data conversion, imzML, common imaging format, converting proprietary formats | PMID:22641155 | Free, Available for download, Freely available | SCR_021642 | 2026-08-12 10:52:22 | 4 | ||||||||||
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Tissue Studio Resource Report Resource Website 1+ mentions |
Tissue Studio (RRID:SCR_023001) | data processing software, image analysis software, software resource, software application | Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis. | Definiens Inc., detect target regions, immunohistochemistry specimen, distinguishes cells and sub-cellular objects | PMID:30930117 | Restricted | SCR_023001 | Definiens Tissue Studio | 2026-08-12 10:52:41 | 2 | |||||||||
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QCAlign Resource Report Resource Website 1+ mentions |
QCAlign (RRID:SCR_023088) | data processing software, image analysis software, software resource, software application | Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas. | QUINT, supports spatial analysis, labelling in series, detect tissue damage regions, detect errors in image acquisitionbrain sections, mouse, rat, reference atlas, | has parent organization: University of Oslo; Oslo; Norway | European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA). | Free, Available for download, Freely available | https://qcalign.readthedocs.io; https://github.com/Neural-Systems-at-UIO/QCAlign | SCR_023088 | 2026-08-12 10:52:50 | 4 |
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